Skill preflight rejects nested reference folders that the SDK accepts #111

Problem

Released pytest-skill-engineering==1.0.1 rejects the Excel CLI skill before sending a model message because its reference documentation is organized in a subdirectory.

Sanitized error:

Skill setup failed before model execution: Invalid references entry (must be a file): ...\excel-cli\references\commands

The skill contains SKILL.md with links to references\commands\*.md. Real, unbilled public-SDK ensure_loaded() / list() checks discover and enable this exact skill directory successfully. The package's additional preflight, not SDK discovery, blocks execution.

Reproduction

Supply a valid skill directory with this shape using client_mode="empty":

excel-cli\SKILL.md
excel-cli\references\commands\range.md
excel-cli\references\commands\table.md

Run the normal public evaluation with that directory in skill_directories. Observe failure before the model send. The sibling Excel MCP skill has flat reference files and passed this check.

Expected behavior

Accept SDK-supported reference subdirectories while retaining safe containment, readability, and applicable symlink/cycle validation. Missing, unsafe, or invalid skills must still fail before spending on a model.

Please verify the reference-directory rules against the Agent Skills specification, add a focused failing regression, and provide a public unbilled preflight path that exercises the same validation as actual evaluation. Consumers should not need a paid evaluation to discover this disagreement.

Impact

A release-only skill-value comparison on 1.0.1 verified three control executions, then stopped on its first CLI treatment without sending a model message. No skill-value conclusion was drawn from the incomplete run. This is a follow-up to #109 / #110, not a request to weaken discovery or isolation checks.